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Graduate School Of Oceanography Annual Report For Fy2017, Uri Graduate School Of Oceanography

Graduate School of Oceanography Publications

Annual report for the Graduate School Oceanography of the University of Rhode Island for the 2017 fiscal year.

Includes research projects by faculty and students, biographies of new faculty, events on the Bay campus and program development and list of donors.

Bifurcation And Global Dynamics Of A Leslie-Gower Type Competitive System Of Rational Difference Equations With Quadratic Terms, V. Hadžiabdić, M. R.S. Kulenović, E. Pilav

Mathematics Faculty Publications

We investigate global dynamics of the following systems of difference equations xn+1 = xn/(A1 + B1xn + C1yn), yn+1+1 = yn2/(A2 + B2xn + C2ynP), n = 0, 1, ., where the parameters A1, A2, B1, B2, C1, and C2 are positive numbers and the initial conditions x0 and y0 are arbitrary nonnegative numbers.This system is a version of the Leslie-Gower competition model for two species. We show that this system has rich dynamics which depends on the part of parametric space.

Genotype And Phenotype In 12 Additional Individuals With Satb2-Associated Syndrome, Yuri A. Zarate, Kalsner, Alice Basinger, Julie R. Jones, Chumei Li, Marta Szybowska, Zhou Luan Xu, Samantha Vergano, Aisling R. Caffrey, Cruz Velasco Gonzalez, Holly Dubbs, Elaine Zackai, Francisca Millan, Aida Telegrafi, Berivan Baskin, Richard Person, Jennifer L. Fish, David B. Everman

Pharmacy Practice and Clinical Research Faculty Publications

SATB2-associated syndrome (SAS) is a multisystemic disorder caused by alterations of the SATB2 gene. We describe the phenotype and genotype of 12 individuals with 10 unique (de novo in 11 of 11 tested) pathogenic variants (1 splice site, 5 frameshift, 3 nonsense, and 2 missense) in SATB2 and review all cases reported in the published literature caused by point alterations thus far. In the cohort here described, developmental delay (DD) with severe speech compromise, facial dysmorphism, and dental anomalies were present in all cases. We also present the third case of tibial bowing in an individual who, just as in …

Lanl Plutonium Assessment, Andrew Elloso, Ryan Murphy, Robert Simpson, Thomas Sullivan

Mechanical Engineering Capstone Design Projects

At the Los Alamos National Laboratory (LANL), low level nuclear waste (LLW) is processed for disposal at the Waste Isolation Pilot Plant. This waste is processed in a glovebox and then placed into a 55 gallon drum and sent to a nondestructive assay (NDA) laboratory to determine if the waste within the drum's reactivity is below 100nCi/g stipulated by the regulation held by the Enviromental Protection Agency (EPA). In several cases every year, the reactivity of the drum is exceeded, thus requiring a costly and dangerous procedural deviation to divide the contents of the drum to reach an acceptable level …

Lab On Paper, Aaron Matarese, Luis Pimentel, Winfield Smith

Mechanical Engineering Capstone Design Projects

This final design report highlights the developments of the Lab on Paper over the past year. The goal is to redesign the Lab on Paper to be more easily manufactured and eliminate the hook effect which causes false negatives in lateral flow assays. Sponsor Labonachip, LLC desires to bring Lab on Paper to market and the easiest way to do so is to adapt it to existing manufacturing lines. By eliminating the hook effect, Lab on Paper will be more accurate and reliable than current lateral flow assays.

The Lab on Paper aims to become a universal diagnostic instrument that …

Tracing Molecular Dephasing In Biological Tissue, Mohammad Mokim, Chris Carruba, Feruz Ganikhanov

Physics Faculty Publications

We demonstrate the quantitative spectroscopic characterization and imaging of biological tissue using coherent time-domain microscopy with a femtosecond resolution. We identify tissue constituents and perform dephasing time (T₂) measurements of characteristic Raman active vibrations. This was shown in subcutaneous mouse fat embedded within collagen rich areas of the dermis and the muscle connective tissue. The demonstrated equivalent spectral resolution (-1) is an order of magnitude better compared to commonly used frequency-domain methods for characterization of biological media. This provides with the important dimensions and parameters in biological media characterization and can become an effective tool in detecting …

Gene Expression As A Dosimeter In Irradiated Drosophila Melanogaster, Samana Shrestha, Adam Vanasse, Leon N. Cooper, Michael Antosh

Physics Faculty Publications

Biological indicators would be of use in radiation dosimetry in situations where an exposed person is not wearing a dosimeter, or when physical dosimeters are insufficient to estimate the risk caused by the radiation exposure. In this work, we investigate the use of gene expression as a dosimeter. Gene expression analysis was done on 15,222 genes of Drosophila melanogaster (fruit flies) at days 2, 10, and 20 postirradiation, with X-ray exposures of 10, 1000, 5000, 10,000, and 20,000 roentgens. Several genes were identified, which could serve as a biodosimeter in an irradiated D. melanogaster model. Many of these genes have …

Amgen Material Handling, Kevin Paiva, Matt Perry, Brandon Fleet

Mechanical Engineering Capstone Design Projects

Amgen is a world leading pharmaceutical company that specializes in biotechnology which develops intravenous or injectable biologic medicines. With an outstanding reputation in the field of safety, quality assurance, superior scientific innovation, and continuous improvement in all aspects, Amgen’s goal is to serve patients cutting edge medications available in today’s market. With this outlook on innovation, Amgen is currently looking into a material handling solution for movement of material between its storage facilities to an IOS9 cleanliness standard laboratory. Such movement includes passing through an airlock which requires the drums containing necessary chemicals for biotechnological production to be cleaned and …

Not Mine Alone, Nor Mine To Own: Some Reflections On The Young Girl, Jacqueline Mabey

Journal of Feminist Scholarship

This essay looks at the role of the young girl in the curatorial practice of Jacqueline Mabey. Mabey reckons with the young girl as the signifier of a spectrum of mutable cultural signifieds and young girls as subjects on their own terms in the two exhibitions under review, Miss World and Utopia Is No Place, Utopia Is Process. In doing so, she recognizes a shift in motivations from an interest in what the young girls mean as a narcissistic reflection to how she could work in service of the development of young girls.

Dna–Carbon Nanotube Complexation Affinity And Photoluminescence Modulation Are Independent, Prakrit V. Jena, Mohammad M. Safaee, Daniel A. Heller, Daniel E. Roxbury

Chemical, Biomolecular, and Materials Engineering Faculty Publications

Short single-stranded DNA (ssDNA) has emerged as the natural polymer of choice for noncovalently functionalizing photoluminescent single-walled carbon nanotubes. In addition, specific empirically identified DNA sequences can be used to separate single species (chiralities) of nanotubes, with an exceptionally high purity. Currently, only limited general principles exist for designing DNA–nanotube hybrids amenable to separation processes, due in part to an incomplete understanding of the fundamental interactions between a DNA sequence and a specific nanotube structure, whereas even less is known in the design of nanotube-based sensors with determined optical properties. We therefore developed a combined experimental and analysis platform on …

Progress Toward Applications Of Carbon Nanotube Photoluminescence, Prakrit V. Jena, Thomas V. Galassi, Daniel E. Roxbury, Daniel A. Heller

Chemical, Biomolecular, and Materials Engineering Faculty Publications

In the fifteen years following the discovery of single-walled carbon nanotube (SWCNT) photoluminescence, investigators have made significant progress in their understanding of the phenomenon and toward the development of applications. The intrinsic potential of semiconducting carbon nanotubes – a family of bright, photostable near infrared (NIR) fluorophores (900–2100 nm) with tunable properties, has motivated their use as optical probes and sensors. In this perspective, we highlight the advances made in the synthesis, processing, modification, separation, and metrology of carbon nanotubes in the context of applications of their photoluminescence.

Single Nanotube Spectral Imaging To Determine Molar Concentrations Of Isolated Carbon Nanotube Species, Thomas V. Galassi, Prakrit V. Jena, Daniel E. Roxbury, Daniel A. Heller

Chemical, Biomolecular, and Materials Engineering Faculty Publications

Electronic and biological applications of carbon nanotubes can be highly dependent on the species (chirality) of nanotube, purity, and concentration. Existing bulk methods, such as absorbance spectroscopy, can quantify sp² carbon based on spectral bands, but nanotube length distribution, defects, and carbonaceous impurities can complicate quantification of individual particles. We present a general method to relate the optical density of a photoluminescent nanotube sample to the number of individual nanotubes. By acquiring 3-dimensional images of nanotubes embedded in a gel matrix with a reducing environment, we quantified all emissive nanotubes in a volume. Via spectral imaging, we assessed structural …

On-Line Adaptive Dynamic Programming For Feedback Control, Xiangnan Zhong

Open Access Dissertations

Stability analysis and controller design are among the most important issues in feedback control problems. Usually, controller design for linear system can be obtained by solving the Riccati equation. However, when comes to the nonlinear control problem, Riccati equation becomes the well-known Hamilton-Jacobi-Bellman (HJB) equation which is difficult to tackle directly. Fortunately, adaptive dynamic programming (ADP) has been widely recognized as one of the “core methodologies” to achieve optimal control in stochastic process in a general case to achieve brain-like intelligent control. Extensive efforts and promising results have been achieved over the past decades. The achievements cover a large variety …

Assessing Hand Hygiene Compliance In Healthcare Workers To Reduce Infectious Disease, Ahmed Salem Alhasani

Open Access Dissertations

Hand hygiene is the first line of defense against the prevalence of infectious diseases in healthcare settings. Therefore, healthcare costs can be reduced. However, having rare incidents of healthcare-associated infections (HAI) does not always mean that hand hygiene compliance is high and at its desired level. This research study aims to develop multi-statistical measurements to assess hand hygiene compliance of the medical and nursing groups at the inpatient wards, 5B, 6B and ICU at the Providence Veterans Affairs Medical Center (PVAMC). The PVAMC was trying to identify whether the few cases or rare incidents of HAI that have been reported …

Direct Substrate Recognition By The Atp-Dependent Chaperone Protease Clpxp And Roles In Proteostasis, Marissa Grace Viola

Open Access Dissertations

The AAA+ (ATPases associated with a variety of cellular activities) protein superfamily includes approximately 30,000 molecular machines powered by adenosine triphosphate (ATP) binding and hydrolysis events, which are important for many cellular processes, including cell division, DNA replication, intracellular transport, and protein quality control. The bacterial AAA+ protein ClpXP is a two component ATP-dependent chaperone-protease that recognizes protein substrates bearing specific recognition signals, subsequently unfolding and degrading them to eliminate unnecessary or misfolded proteins. Since degradation is irreversible, highly specific recognition motifs are needed to ensure intentional engagement. A common strategy to facilitate recognition of substrates by AAA+ ATPases is …

Using Natural Products To Treat Resistant And Persistent Bacterial Infections, Robert W. Deering

Open Access Dissertations

Antimicrobial resistance is a growing threat to human health both worldwide and in the United States. Most concerning is the emergence of multi-drug resistant (MDR) bacterial pathogens, especially the ‘ESKAPE’ pathogens for which treatment options are dwindling. To complicate the problem, approvals of antibiotic drugs are extremely low and many research and development efforts in the pharmaceutical industry have ceased, leaving little certainty that critical new antibiotics are nearing the clinic. New antibiotics are needed to continue treating these evolving infections. In addition to antibiotics, approaches that aim to inhibit or prevent antimicrobial resistance could be useful. Also, studies that …

Biological Process: Characterization, Establishment Of Shelf Life And Optimizing Method Transfers, Syama S. Adhibhatta

Open Access Dissertations

Biological processes are complex and can be modeled using combination of linear and non-linear models. During the cell culture process, cells may change or evolve and it is extremely important to understand the variability of the process to manufacture consistent product. In order to maximize the output from the process, process parameters need to be characterized and optimized. Data from process involves linear and non-linear patterns and some of the parameters are auto-correlated. One of the objectives of study was to compare Unsupervised Dimesional Reduction methods to Supervised machine learning algorithms applied to biopharmaceutical manufacturing process data and suggest a …

Coastal Observations From A New Vantage Point, Joseph Salisbury, Curtiss Davis, Angela Erb, Chuanmin Hu, Charles Gatebe, Carolyn Jordan, Zhongping Lee, Antonio Mannino, Colleen B. Mouw, Crystal Schaaf, Blake A. Schaeffer, Maria Tzortziou

Graduate School of Oceanography Faculty Publications

No abstract provided.

Using Polyethylene Passive Samplers To Study The Partitioning And Fluxes Of Pbdes In An Urban River, Mohammed A. Khairy, Rainer Lohmann

Graduate School of Oceanography Faculty Publications

In the aquatic environment, the behavior of hydrophobic organic contaminants (HOCs), such as polybrominated diphenyl ethers (PBDEs), depends on the congeners’ physicochemical properties, environmental conditions and the presence of competing natural sorbents, including particulate and dissolved organic carbon (DOC) and black carbon (BC). Although BC is known as an important sedimentary sorbent for HOCs, its affinity for PBDEs has been poorly constrained. To better understand the biogeochemical controls on PBDEs, 12 PBDE congeners were measured in air, water, sediment and porewater of the lower Passaic River. BDE-47 and BDE-99 dominated in all media. In sediments and water, the dual OC …

Changes In The Size Structure Of Marine Fish Communities, Richard J. Bell, Jeremy Collie, Trevor A. Branch, Michael J. Fogarty, Coilin Minto, Daniel Ricard

Graduate School of Oceanography Faculty Publications

Marine ecosystems have been heavily impacted by fishing pressure, which can cause major changes in the structure of communities. Fishing directly removes biomass and causes secondary effects such as changing predatory and competitive interactions and altering energy pathways, all of which affect the functional groups and size distributions of marine ecosystems. We conducted a meta-analysis of eighteen trawl surveys from around the world to identify if there have been consistent changes in size-structure and life history groups across ecosystems. Declining biomass trends for larger fish and invertebrates were present in nine systems, all in the North Atlantic, while seven ecosystems …

Uri Undergraduate And Graduate Course Catalog 2017-2018, University Of Rhode Island

URI Course Catalogs Archive

This is a downloadable PDF version of the University of Rhode Island course catalog.

Hand Motion Detection In Fnirs Neuroimaging Data, Mohammadreza Abtahi, Amir Mohammad Amiri, Dennis Byrd, Kunal Mankodiya

Electrical, Computer, and Biomedical Engineering Faculty Publications

As the number of people diagnosed with movement disorders is increasing, it becomes vital to design techniques that allow the better understanding of human brain in naturalistic settings. There are many brain imaging methods such as fMRI, SPECT, and MEG that provide the functional information of the brain. However, these techniques have some limitations including immobility, cost, and motion artifacts. One of the most emerging portable brain scanners available today is functional near-infrared spectroscopy (fNIRS). In this study, we have conducted fNIRS neuroimaging of seven healthy subjects while they were performing wrist tasks such as flipping their hand with the …